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dbSNP Short Genetic Variations

Reference SNP (rs) Report


This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.


Current Build 151

Released July 17, 2018

Homo sapiens
chr7:107704382 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Variation Type
SNV Single Nucleotide Variation
T=0.00001 (3/217818, GnomAD)
T=0.0000 (1/62352, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC26A4 : Stop Gained
5 citations
Genomic View
See rs on genome

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 7 NC_000007.14:g.107704382C>T
GRCh37.p13 chr 7 NC_000007.13:g.107344827C>T
SLC26A4 RefSeqGene NG_008489.1:g.48748C>T
Gene: SLC26A4, solute carrier family 26 member 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC26A4 transcript NM_000441.1:c.208...


Q [CAA] > * [TAA] Coding Sequence Variant
pendrin NP_000432.1:p.Gln...


Q (Gln) > * (Ter) Stop Gained
SLC26A4 transcript variant X3 XM_006716025.3:c. N/A Genic Downstream Transcript Variant
SLC26A4 transcript variant X1 XM_005250425.2:c....


Q [CAA] > * [TAA] Coding Sequence Variant
pendrin isoform X1 XP_005250482.1:p....


Q (Gln) > * (Ter) Stop Gained
SLC26A4 transcript variant X2 XM_017012318.1:c....


Q [CAA] > * [TAA] Coding Sequence Variant
pendrin isoform X2 XP_016867807.1:p....


Q (Gln) > * (Ter) Stop Gained

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 186741 )
ClinVar Accession Disease Names Clinical Significance
RCV000169591.1 Pendred's syndrome Likely-Pathogenic

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 217818 C=0.99999 T=0.00001
The Genome Aggregation Database European Sub 112950 C=1.00000 T=0.00000
The Genome Aggregation Database Asian Sub 45084 C=0.9999 T=0.0001
The Genome Aggregation Database American Sub 32276 C=1.0000 T=0.0000
The Genome Aggregation Database African Sub 13474 C=1.0000 T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9094 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 4940 C=1.000 T=0.000
The Exome Aggregation Consortium Global Study-wide 62352 C=1.0000 T=0.0000
The Exome Aggregation Consortium Europe Sub 32588 C=1.0000 T=0.0000
The Exome Aggregation Consortium Asian Sub 16490 C=0.9999 T=0.0001
The Exome Aggregation Consortium African Sub 6682 C=1.000 T=0.000
The Exome Aggregation Consortium American Sub 6074 C=1.000 T=0.000
The Exome Aggregation Consortium Other Sub 518 C=1.00 T=0.00

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T Note
GRCh38.p7 chr 7 NC_000007.14:g.107704382C= NC_000007.14:g.10770438...


GRCh37.p13 chr 7 NC_000007.13:g.107344827C= NC_000007.13:g.10734482...


SLC26A4 RefSeqGene NG_008489.1:g.48748C= NG_008489.1:g.48748C>T
SLC26A4 transcript NM_000441.1:c.2086C= NM_000441.1:c.2086C>T
SLC26A4 transcript variant X1 XM_005250425.2:c.2086C= XM_005250425.2:c.2086C>T
SLC26A4 transcript variant X1 XM_005250425.1:c.2086C= XM_005250425.1:c.2086C>T
SLC26A4 transcript variant X2 XM_017012318.1:c.2008C= XM_017012318.1:c.2008C>T
pendrin NP_000432.1:p.Gln696= NP_000432.1:p.Gln696Ter
pendrin isoform X1 XP_005250482.1:p.Gln696= XP_005250482.1:p.Gln696Ter
pendrin isoform X2 XP_016867807.1:p.Gln670= XP_016867807.1:p.Gln670Ter

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 Frequency, 4 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1688900784 Apr 01, 2015 (144)
2 CLINVAR ss1751114130 May 21, 2015 (136)
3 GNOMAD ss2736693890 Nov 08, 2017 (151)
4 ILLUMINA ss3022767441 Nov 08, 2017 (151)
5 The Exome Aggregation Consortium NC_000007.13 - 107344827 Jul 20, 2018 (151)
6 The Genome Aggregation Database NC_000007.13 - 107344827 Jul 20, 2018 (151)
7 ClinVar RCV000169591.1 Jul 20, 2018 (151)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs786204742 Jul 01, 2015 (136)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
8979454, 5708625, ss1688900784, ss2736693890, ss3022767441 NC_000007.13:107344826:C= NC_000007.14:107704381:C= (self)
ss1751114130 NC_000007.14:107704381:C= NC_000007.14:107704381:C= (self)
8979454, 5708625, ss1688900784, ss2736693890, ss3022767441 NC_000007.13:107344826:C>T NC_000007.14:107704381:C>T (self)
RCV000169591.1, ss1751114130 NC_000007.14:107704381:C>T NC_000007.14:107704381:C>T (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

5 citations for rs752807925
PMID Title Author Year Journal
21961810 Extremely discrepant mutation spectrum of SLC26A4 between Chinese patients with isolated Mondini deformity and enlarged vestibular aqueduct. Huang S et al. 2011 Journal of translational medicine
22289209 Genetic diagnosis and cochlear implantation for patients with nonsyndromic hearing loss and enlarged vestibular aqueduct. Lai R et al. 2012 The Journal of laryngology and otology
23918157 Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China. Chai Y et al. 2013 American journal of medical genetics. Part A
24612839 Developing regional genetic counseling for southern Chinese with nonsyndromic hearing impairment: a unique mutational spectrum. Chen K et al. 2014 Journal of translational medicine
24913939 Genetic counseling and prenatal diagnosis for hereditary hearing loss in high-risk families. Yin A et al. 2014 International journal of pediatric otorhinolaryngology

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e